I managed to find the solution. Which was not the id's in the .dose-files but the markers (positions) in the info-files. After imputation, SNPs with several alleles, or with additional indels or deletions, are separated into different rows in the .vcf-files, meaning that each "SNP" in the ...

I think we found the solution. The vcf-files contain several variants of the same marker, e.g. biallelic SNPs, indels or deletion, separated on several lines. This means that one marker (on position) may appear several times in the vcf-file. When removing the "duplicates", the program seem...